ProteomeScout

GitHub Paper

Matlock MK, Holehouse AS, Naegle KM. ProteomeScout: a repository and analysis resource for post-translational modifications and proteins. Nucleic Acids Res. 2015;43(Database issue):D521-D530. doi: 10.1093/nar/gku1154.

ProteomeScoutAPI

GitHub Paper

Holehouse AS, Naegle KM. Reproducible Analysis of Post-Translational Modifications in Proteomes--Application to Human Mutations. PLoS One. 2015;10(12):e0144692. doi: 10.1371/journal.pone.0144692.

KSTAR

GitHub Documentation Paper

Crowl S, Jordan BT, Ahmed H, Ma CX, Naegle KM. KSTAR: An algorithm to predict patient-specific kinase activities from phosphoproteomic data. Nat Commun. 2022;13(1):4283. doi: 10.1038/s41467-022-32017-5.

CoDIAC

GitHub Documentation Paper

Kandoor A, Martinez G, Hitchcock JM, Angel S, Campbell L, Rizvi S, Naegle KM. CoDIAC: A comprehensive approach for interaction analysis provides insights into SH2 domain function and regulation. Sci Signal. 2025;18(913):eads8396. doi: 10.1126/scisignal.ads8396.

PTM-POSE

GitHub Documentation Paper

Crowl S, Coleman MB, Chaphiv A, Jordan BT, Naegle KM. Systematic analysis of the effects of splicing on the diversity of post-translational modifications in protein isoforms using PTM-POSE. Cell Syst. 2025;16(7):101318. doi: 10.1016/j.cels.2025.101318.

DANSy

GitHub Documentation Paper

Shimpi AA, Naegle KM. Uncovering the domain language of protein functionality and cell phenotypes using DANSy. bioRxiv [Preprint]. 2025 Jul 1:2024.12.04.626803. doi: 10.1101/2024.12.04.626803.

OpenEnsembles

GitHub Documentation Paper

Ronan T, Anastasio S, Qi Z, Tavares PHS, Sloutsky R, Naegle KM. OpenEnsembles: A Python Resource for Ensemble Clustering. J Mach Learn Res. 2018;19(26):1-6.

ASPEN

GitHub Paper

Sloutsky R, Naegle KM. ASPEN, a methodology for reconstructing protein evolution with improved accuracy using ensemble models. eLife. 2019;8:e47676. doi: 10.7554/eLife.47676.